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Detailed information for vg0816117066:

Variant ID: vg0816117066 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16117066
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGGTTTATCTAAACTTAAGAAAGATCTTGATTTGGTTTGTACACCGTGTCATCATGCTAAGATGGTTGCTTCTTCACATGCTCCTATTATTTCTGTGA[G/T]
GACGGATGCACCGGGACAGCTATTACACATGGACACTGTTGGTCCAGCTAGAGTGCAATCTGTTGGAGGAAAGTGGTATGTGTGGGTTATTGTTCACGAT

Reverse complement sequence

ATCGTGAACAATAACCCACACATACCACTTTCCTCCAACAGATTGCACTCTAGCTGGACCAACAGTGTCCATGTGTAATAGCTGTCCCGGTGCATCCGTC[C/A]
TCACAGAAATAATAGGAGCATGTGAAGAAGCAACCATCTTAGCATGATGACACGGTGTACAAACCAAATCAAGATCTTTCTTAAGTTTAGATAAACCACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.40%	14.00%	10.11%	51.54%	NA
All Indica	2759	5.80%	3.00%	15.91%	75.28%	NA
All Japonica	1512	56.50%	33.00%	1.12%	9.39%	NA
Aus	269	3.30%	20.10%	6.32%	70.26%	NA
Indica I	595	12.30%	0.50%	12.27%	74.96%	NA
Indica II	465	6.50%	4.70%	18.71%	70.11%	NA
Indica III	913	1.10%	2.00%	18.07%	78.86%	NA
Indica Intermediate	786	6.10%	5.00%	14.50%	74.43%	NA
Temperate Japonica	767	96.30%	0.90%	0.39%	2.35%	NA
Tropical Japonica	504	6.00%	74.40%	1.59%	18.06%	NA
Japonica Intermediate	241	35.30%	48.50%	2.49%	13.69%	NA
VI/Aromatic	96	92.70%	4.20%	1.04%	2.08%	NA
Intermediate	90	43.30%	23.30%	4.44%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816117066	G -> T	LOC_Os08g26450.1	missense_variant ; p.Arg737Met; MODERATE	nonsynonymous_codon ; R737M	Average:8.232; most accessible tissue: Callus, score: 29.112	possibly damaging	-1.836	TOLERATED	1.00
vg0816117066	G -> DEL	LOC_Os08g26450.1	N	frameshift_variant	Average:8.232; most accessible tissue: Callus, score: 29.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816117066	NA	2.79E-09	mr1002_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	5.60E-07	mr1042_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	8.99E-08	mr1047_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.78E-08	mr1189_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.41E-06	mr1268_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.90E-07	mr1308_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	8.79E-13	mr1361_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	6.21E-06	mr1397_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.30E-06	mr1449_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.31E-06	mr1509_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	3.61E-10	mr1543_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	2.10E-10	mr1742_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.94E-07	mr1817_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	5.13E-06	mr1853_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0816117066	NA	1.58E-08	mr1871_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251